4) Is it possible to get these default again? (changed by custom theme)

Try this command:/startup_toolbar -r

+ I want to change the color of my own messages in channels.

You have to edit the theme file for this or create your own theme. See above.

+ It connects with my bnc AND to qnet, I only want the bnc-connection though.. How to disable the other one?

Right click into the q-net status window and un-check always connect to Quakenet.

In 5.xx I didn't get this 'end of /whois' and I don't want it now

I think you had a different theme in your 5.xx
However 6.00 only supports 1 theme at the moment. So you have to change the theme or create your own one. In the .mts file the line raw.318 <c3>::: End of Whois is for the end of whois. Remove the stuff after the raw.318 and reload the theme. Note: We will update our greyworld theme in every version (so your changes get lost if you don't safe it in a different file), but we cannot create different versions for everyone.

I unchecked 'show MOTD' anyways, why is it still there?

Will be fixed in our theme in the next version. I think you have to live with it for now.

+ when I join a channel I get a weird msg in the window, e.g. '[20:12] § 1050208334' , '[19:36] § 1223155067', etc.. ( = ctrl+k)

I am not sure what this should be? Does this happen in every channel when you join it?

menu nicklist,query {
-
More slaps
.Rickrolling:me rickrolls $1
.UNIX manual:me slaps $1 around a bit with a small 50lb UNIX manual
.<own>:me slaps $1 around a bit with $$?"... with ...?"
}

Put this as a new .mrc file into your scripts dir to use it.

Some explanation:
The above code adds a new separator ("-") and a submenu "More slaps" to your nicklist and query context menus. Within that submenu are three items (starting with a dot, marking the submenu level; two dots would be under the previous item with one dot and so on).

An item has the following syntax:(label):(action)

So, if you choose "Rickrolling" in a query with Chris1-, Gamers.IRC will execute this command:

Sure. You can change the color of the black nicks in the Address Book. (alt+b)
Switch to the tab nick colors and change the black colors. Note: There can be different colors for the nicklist and messages.